Contamination of genomic databases by HIV-1 and its possible consequences. A study in Bioinformatics.

Peer-reviewed

Bioinformatics: making large-scale science happen

Bionformatics is a rapidly evolving research field dedicated toanalyzing and managing biological data with computational resources. This paperaims to overview some of the processes and applications currently implementedat CCiT-UB¿s Bioinformatics Unit, focusing mainly on the areas of Genomics,Transcriptomics and Proteomics

Pathway databases and tools for their exploitation: benefits, current limitations and challenges

In past years, comprehensive representations of cell signalling pathways have been developed by manual curation from literature, which requires huge effort and would benefit from information stored in databases and from automatic retrieval and integration methods. Once a reconstruction of the network of interactions is achieved, analysis of its structural features and its dynamic behaviour can take place. Mathematical modelling techniques are used to simulate the complex behaviour of cell signalling networks, which ultimately sheds light on the mechanisms leading to complex diseases or helps in the identification of drug targets. A variety of databases containing information on cell signalling pathways have been developed in conjunction with methodologies to access and analyse the data. In principle, the scenario is prepared to make the most of this information for the analysis of the dynamics of signalling pathways. However, are the knowledge repositories of signalling pathways ready to realize the systems biology promise? In this article we aim to initiate this discussion and to provide some insights on this issue.

The EU-ADR Web Platform: delivering advanced pharmacovigilance tools

PURPOSE: Pharmacovigilance methods have advanced greatly during the last decades, making post-market drug assessment an essential drug evaluation component. These methods mainly rely on the use of spontaneous reporting systems and health information databases to collect expertise from huge amounts of real-world reports. The EU-ADR Web Platform was built to further facilitate accessing, monitoring and exploring these data, enabling an in-depth analysis of adverse drug reactions risks.METHODS: The EU-ADR Web Platform exploits the wealth of data collected within a large-scale European initiative, the EU-ADR project. Millions of electronic health records, provided by national health agencies, are mined for specific drug events, which are correlated with literature, protein and pathway data, resulting in a rich drug-event dataset. Next, advanced distributed computing methods are tailored to coordinate the execution of data-mining and statistical analysis tasks. This permits obtaining a ranked drug-event list, removing spurious entries and highlighting relationships with high risk potential.RESULTS: The EU-ADR Web Platform is an open workspace for the integrated analysis of pharmacovigilance datasets. Using this software, researchers can access a variety of tools provided by distinct partners in a single centralized environment. Besides performing standalone drug-event assessments, they can also control the pipeline for an improved batch analysis of custom datasets. Drug-event pairs can be substantiated and statistically analysed within the platform's innovative working environment.CONCLUSIONS: A pioneering workspace that helps in explaining the biological path of adverse drug reactions was developed within the EU-ADR project consortium. This tool, targeted at the pharmacovigilance community, is available online at https://bioinformatics.ua.pt/euadr/. Copyright © 2012 John Wiley & Sons, Ltd.

Do protein–protein interaction databases identify moonlighting proteins?

One of the most striking results of the human (and mammalian) genomes is the low number of protein-coding genes. To-date, the main molecular mechanism to increase the number of different protein isoforms and functions is alternative splicing. However, a less-known way to increase the number of protein functions is the existence of multifunctional, multitask, or ‘‘moonlighting’’, proteins. By and large, moonlighting proteins are experimentally disclosed by serendipity. Proteomics is becoming one of the very active areas of biomedical research, which permits researchers to identify previously unseen connections among proteins and pathways. In principle, protein–protein interaction (PPI) databases should contain information on moonlighting proteins and could provide suggestions to further analysis in order to prove the multifunctionality. As far as we know, nobody has verified whether PPI databases actually disclose moonlighting proteins. In the present work we check whether well-established moonlighting proteins present in PPI databases connect with their known partners and, therefore, a careful inspection of these databases could help to suggest their different functions. The results of our research suggest that PPI databases could be a valuable tool to suggest multifunctionality.

Biblio-MetReS: A bibliometric network reconstruction application and server

Background: Reconstruction of genes and/or protein networks from automated analysis of the literature is one of the current targets of text mining in biomedical research. Some user-friendly tools already perform this analysis on precompiled databases of abstracts of scientific papers. Other tools allow expert users to elaborate and analyze the full content of a corpus of scientific documents. However, to our knowledge, no user friendly tool that simultaneously analyzes the latest set of scientific documents available on line and reconstructs the set of genes referenced in those documents is available. Results: This article presents such a tool, Biblio-MetReS, and compares its functioning and results to those of other user-friendly applications (iHOP, STRING) that are widely used. Under similar conditions, Biblio-MetReS creates networks that are comparable to those of other user friendly tools. Furthermore, analysis of full text documents provides more complete reconstructions than those that result from using only the abstract of the document. Conclusions: Literature-based automated network reconstruction is still far from providing complete reconstructions of molecular networks. However, its value as an auxiliary tool is high and it will increase as standards for reporting biological entities and relationships become more widely accepted and enforced. Biblio- MetReS is an application that can be downloaded from http://metres.udl.cat/. It provides an easy to use environment for researchers to reconstruct their networks of interest from an always up to date set of scientific documents.

REGSTATTOOLS: freeware statistical tools for the analysis of disease population databases used in health and social studies

Background: The repertoire of statistical methods dealing with the descriptive analysis of the burden of a disease has been expanded and implemented in statistical software packages during the last years. The purpose of this paper is to present a web-based tool, REGSTATTOOLS http://regstattools.net intended to provide analysis for the burden of cancer, or other group of disease registry data. Three software applications are included in REGSTATTOOLS: SART (analysis of disease"s rates and its time trends), RiskDiff (analysis of percent changes in the rates due to demographic factors and risk of developing or dying from a disease) and WAERS (relative survival analysis). Results: We show a real-data application through the assessment of the burden of tobacco-related cancer incidence in two Spanish regions in the period 1995-2004. Making use of SART we show that lung cancer is the most common cancer among those cancers, with rising trends in incidence among women. We compared 2000-2004 data with that of 1995-1999 to assess percent changes in the number of cases as well as relative survival using RiskDiff and WAERS, respectively. We show that the net change increase in lung cancer cases among women was mainly attributable to an increased risk of developing lung cancer, whereas in men it is attributable to the increase in population size. Among men, lung cancer relative survival was higher in 2000-2004 than in 1995-1999, whereas it was similar among women when these time periods were compared. Conclusions: Unlike other similar applications, REGSTATTOOLS does not require local software installation and it is simple to use, fast and easy to interpret. It is a set of web-based statistical tools intended for automated calculation of population indicators that any professional in health or social sciences may require.

BioSWR - Semantic Web services Registry for Bioinformatics

Article About the Authors Metrics Comments Related Content Abstract Introduction Functionality Implementation Discussion Acknowledgments Author Contributions References Reader Comments (0) Figures Abstract Despite of the variety of available Web services registries specially aimed at Life Sciences, their scope is usually restricted to a limited set of well-defined types of services. While dedicated registries are generally tied to a particular format, general-purpose ones are more adherent to standards and usually rely on Web Service Definition Language (WSDL). Although WSDL is quite flexible to support common Web services types, its lack of semantic expressiveness led to various initiatives to describe Web services via ontology languages. Nevertheless, WSDL 2.0 descriptions gained a standard representation based on Web Ontology Language (OWL). BioSWR is a novel Web services registry that provides standard Resource Description Framework (RDF) based Web services descriptions along with the traditional WSDL based ones. The registry provides Web-based interface for Web services registration, querying and annotation, and is also accessible programmatically via Representational State Transfer (REST) API or using a SPARQL Protocol and RDF Query Language. BioSWR server is located at http://inb.bsc.es/BioSWR/and its code is available at https://sourceforge.net/projects/bioswr/​under the LGPL license.

Sensitivity of simulation results to competing SAM updates

Recently there has been a renewed research interest in the properties of non survey updates of input-output tables and social accounting matrices (SAM). Along with the venerable and well known scaling RAS method, several alternative new procedures related to entropy minimization and other metrics have been suggested, tested and used in the literature. Whether these procedures will eventually substitute or merely complement the RAS approach is still an open question without a definite answer. The performance of many of the updating procedures has been tested using some kind of proximity or closeness measure to a reference input-output table or SAM. The first goal of this paper, in contrast, is the proposal of checking the operational performance of updating mechanisms by way of comparing the simulation results that ensue from adopting alternative databases for calibration of a reference applied general equilibrium model. The second goal is to introduce a new updatin! g procedure based on information retrieval principles. This new procedure is then compared as far as performance is concerned to two well-known updating approaches: RAS and cross-entropy. The rationale for the suggested cross validation is that the driving force for having more up to date databases is to be able to conduct more current, and hopefully more credible, policy analyses.

Giving SBML support to ByoDyn

Report for the scientific stay at the California Institute of Technology during the summer of 2005. ByoDyn is a tool for simulating the dynamical expression of gene regulatory networks (GRNs) and for parameter estimation in uni- and multicellular models. A software support was carried out describing GRNs in the Systems Biology Markup Language (SBML). This one is a computer format for representing and storing computational models of biochemical pathways in software tools and databases. Supporting this format gives ByoDyn a wide range of possibilities to study the dynamical properties of multiple regulatory pathways.

Trials, tricks and transparency: how disclosure rules affect clinical knowledge

Scandals of selective reporting of clinical trial results by pharmaceutical firms have underlined the need for more transparency in clinical trials. We provide a theoretical framework which reproduces incentives for selective reporting and yields three key implications concerning regulation. First, a compulsory clinical trial registry complemented through a voluntary clinical trial results database can implement full transparency (the existence of all trials as well as their results is known). Second, full transparency comes at a price. It has a deterrence effect on the incentives to conduct clinical trials, as it reduces the firms'gains from trials. Third, in principle, a voluntary clinical trial results database without a compulsory registry is a superior regulatory tool; but we provide some qualified support for additional compulsory registries when medical decision-makers cannot anticipate correctly the drug companies' decisions whether to conduct trials. Keywords: pharmaceutical firms, strategic information transmission, clinical trials, registries, results databases, scientific knowledge JEL classification: D72, I18, L15

Sistema de Informació i Gestió Integral de la Producció Pesquera Internacional (SIGIPPI)

Des de la ciència geogràfica combinada amb el coneixement biològic i comercial, aquest projecte pretén crear una eina basada en la biogeografia i les últimes tecnologies de la Informació Geogràfica, que permetrà a l’usuari disposar de informació actualitzada per cada espècie amb interès comercial. El projecte es basa en el desenvolupament d’una aplicació web de consulta, entrada i actualització de dades referents a la producció pesquera internacional. Les eines utilitzades són les bases de dades MySQL i PostgreSQL i programació web amb html, php i javacript. Aquesta aplicació està pensada per ser accessible des de qualsevol ordinador amb connexió a internet i es subdivideix en tres sub-aplicacions. La primera sub-aplicació es basa en l’entrada d’espècies a partir de l’estructura taxonòmica. Partint de l’arbre taxonòmic, l’usuari té la possibilitat d’entrar, eliminar o modificar qualsevol tàxon o espècie. La segona subaplicació és una eina de digitalització cartogràfica on-line on l’usuari podrà marcar, eliminar o modificar sobre un mapa les localitzacions de les espècies que estiguin entrades en la sub-aplicació anterior. Finalment, la tercera sub-aplicació és una eina d’entrada de dades quinzenals referent als comportaments pel que fa tan a les dimensions com a les disponibilitats de pesca per cada espècie i localització.

Recepción y difusión internacionales de Mercè Rodoreda: obra original, crítica y traducción

RESUM Recepción y difusión internacionales de Mercè Rodoreda: obra original, crítica y traducción té per objecte determinar la recepció i la difusió de l’obra original de Mercè Rodoreda, així com de l’obra crítica i de les traduccions, en el context internacional a partir de la interpretació de quatre bases de dades: obra literària de Mercè Rodoreda, obra crítica de Mercè Rodoreda i la seva obra, traductors i traduccions en funció de la llengua i de l’obra i, per últim, presència documental de Mercè Rodoreda a les Biblioteques Nacionals del món. El treball de recerca s’estructura de la següent manera. En primer lloc, plantegem i delimitem el tema, els objectius, la metodologia i la descripció de les bases de dades. Acte seguit, interpretem les bases de dades i exposem algunes consideracions. A continuació, presentem les conclusions finals que hem desenvolupat en cadascun dels àmbits en els que se centra la nostra recerca, així com el projecte de tesi doctoral i les noves línies de recerca. Per últim, exposem la bibliografia i els annexes, en els que incloem les bases de dades i reproduim els estudis traductològics comentats en el treball. Amb l’elaboració d’aquest treball de recerca pretenem, entre d’altres, donar a conèixer els gèneres literaris que va cultivar Mercè Rodoreda; recopilar l’obra crítica al voltant de l’autora i distingir la seva temàtica per determinar el nombre d’estudis crítics sobre traducció; identificar quins títols de l’obra de Mercè Rodoreda s’han traslladat a altres llengües, així com confirmar quina és l’obra més traduïda i quines les llengües a les que s’ha traslladat la seva obra; i, per últim, constatar la presència d’obres originals, estudis crítics i traduccions a les Biblioteques Nacionals del món i identificar-ne les possibles àrees d’expansió.